Rarefy: Rarefy the OTU table to an equal sequencing depth

Description Usage Arguments Value Author(s) References See Also Examples

Description

GUniFrac is also sensitive to different sequencing depth. To compare microbiomes on an equal basis, rarefaction might be used.

Usage

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Rarefy(otu.tab, depth = min(rowSums(otu.tab)))

Arguments

otu.tab

OTU count table, row - n sample, column - q OTU

depth

Required sequencing depth; If not specified, the lowest sequencing depth is used.

Value

Return a LIST containing:

otu.tab.rff

Rarefied OTU table

discard

IDs of samples that does not reach the specified sequencing depth

Author(s)

Jun Chen <chen.jun2@mayo.edu>

References

Jun Chen et al. (2012). Associating microbiome composition with environmental covariates using generalized UniFrac distances. 28(16): 2106–2113.

See Also

GUniFrac, PermanovaG

Examples

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data(throat.otu.tab)
# Rarefaction
otu.tab.rff <- Rarefy(throat.otu.tab, 1024)$otu.tab.rff

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-3
Loading required package: ape

GUniFrac documentation built on May 2, 2019, 2:08 a.m.